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Study Suggests Possibility of Gleaning Epigenetic Insights from Newborn Bloodspot Samples

NEW YORK (GenomeWeb News) – Blood spot samples collected from babies at birth could offer a means of uncovering epigenetic patterns that stick with individuals over the long term, new research suggests.

In a study appearing online today in Genome Research, researchers from the UK, Sweden, and Germany demonstrated that it's possible to assess DNA methylation patterns using genetic material retrieved from so-called Guthrie cards — swatches of filter paper spotted with newborn blood as a means of screening for diseases such as phenylketonuria, cystic fibrosis, and sickle cell disease.

The team's comparison of methylation profiles in Guthrie bloodspot samples and in blood samples collected from the same individuals three later indicated that DNA methylation varies from one individual to the next. Still, each individual's methylome appeared to remain fairly similar over time, hinting that newborn samples might provide a chance to detect clinically relevant epigenetic patterns prior to the onset of disease.

"These findings suggest that disease-relevant epigenetic variation could be detected at birth, i.e., before overt clinical disease," co-senior authors Vardhman Rakyan and David Leslie, both based at Queen Mary University of London, and their colleagues said. "Guthrie card methylomics offers a potentially powerful and cost-effective strategy for studying the dynamics of inter-individual epigenomic variation in a range of common human diseases," they added.

Over the past decade or more, Guthrie cards have become standard at American hospitals, the researchers explained.

Their widespread use in the US and some other countries prompted the group to hit on the notion of trying to use these samples for longitudinal epigenetic studies as an alternative to doing more costly and time-consuming prospective trials.

"Remarkably, in many cases Guthrie cards are being stored indefinitely," they wrote. "This led us to consider genome-wide DNA methylation profiling — DNA methylomics — of Guthrie cards as a means of investigating the origins of disease-associated epigenetic variation."

Using DNA extracted from cord blood-spotted Guthrie cards collected as part of a diabetes study in Sweden in 2000, the team took a crack at using two different methods for assessing methylation: Illumina 450K arrays and a sequencing-based method that involves immunoprecipitation of methylated DNA.

After hammering out each of the methylation-profiling protocols and ensuring that they provided consistent results, researchers focused in on three individuals enrolled in the Swedish study.

To look at the stability of various methylation marks over time in the same individual, the team determined cytosine methylation patterns for each of the three children at birth using DNA from Guthrie cards and compared these profiles to methylation patterns present in whole-blood samples taken when the children were three years old.

In addition to the methylation profiling, the team did SNP-based genotyping on DNA from the same individuals with Illumina's Omni2.5S array.

The group saw inter-individual variability in methylation patterns. But each individual's methylation marks stay fairly stable over time: most of the sites in the genome where methylation profiles varied from one individual to the next at birth showed similar variation in the three-year olds.

"This demonstrates, for the first time, the existence of temporally stable inter-individual epigenetic variation that is present at birth," the team noted. "These [differentially methylated regions] were found across the genome, associated with a variety of genomic elements including promoters and [CpG islands], but also intergenic regions."

And, they say, the possibility of deciphering long-lasting epigenetic marks at birth could prove useful for future studies aimed at understanding the influence of epigenetics on traits and diseases that develop later in life.

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